Hi!

As I'm not aware of such tools, I would recommend using ensembl via ensembl.org.

You can query the cds length from ensenbl's BioMart or directly from the page.

I hope it helps.

BR,

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Oyediran

Hi,

I am not aware of a tool, but I can tell you how to get the information you want for an entire genome. Download the file with known genes (all exons of all known genes) in gtf or bed format from the ucsc genome browser, more specifically the Table browser. I recommend using the bed format, which has the chromosome number in the first column, the start and stop positions in the second and third column, and a gene identifier in the fourth column. You need to write a script or use R to compute the length of each exon and then sum them up per genes.

The small issue with this is that the bed file does not include the standard HUGO gene symbols. Instead, it uses a different gene ID which usually has to be translated into the gene symbols most biologists will recognize. You can do that by downloading the kgXref table from the genome/table browser, which lists the alternative names and IDs for each gene. You can select to download the known gene ID (kgID) and the geneSymbol only in a simple text format. You can then match the gene IDs from the bed file to the gene symbols found in this table.

MIZ